Current revision

This list is intended mostly for de novo splice site / transcript / gene prediction in newly sequenced genomes. At the same time tools listed below often are used in other pipelines such as transcript quantification or SNP discovery.

Currently the most widely used program for RNA-Seq mapping. Output often processed with Cufflinks.
Latest version supports TopHat detection of insertions and deletions using RNA-Seq data.
Supports mixed length reads (suitable i.e. for 454 data)

last can map reads with indels and truncate large parts of the reads (highly sensitive but with lower specificity). For example it can report just 30 nucleotide long matches out of 54nn long queries.
Output needs to be filtered from spurious matches.

It does not have multiple processor option, so for faster mapping one has to split fastq file(s), run last in parallel and combine the results (or use Hadoop).

Since version 149 it is possible to get SAM output by two step procedure: